Lineage assignment

Pangolin and Nextclade

Lineage assigment table using Pangolin and Nextclade of all samples.

Sample Coverage Pangolin Scorpio Nextclade WHO clade Note
ERR12411100 99.89% AY.98.1 Delta (B.1.617.2-like) AY.98.1 Delta Usher placements: AY.98.1(1/1)
ERR12411099 99.82% BA.1 Delta (B.1.617.2-like) +K417N AY.98.1 Delta Usher placements: BA.1(1/1); scorpio lineage B.1.617.2 conflicts with inference lineage BA.1
ERR12411105 99.72% B.1.1.529 Delta (B.1.617.2-like) +K417N BA.5 Omicron Usher placements: B.1.1.529(1/1); scorpio lineage B.1.617.2 conflicts with inference lineage B.1.1.529
ERR12411106 99.72% B.1.1.529 Delta (B.1.617.2-like) +K417N BA.5 Omicron Usher placements: B.1.1.529(1/1); scorpio lineage B.1.617.2 conflicts with inference lineage B.1.1.529
ERR12411098 99.84% BA.1 Delta (B.1.617.2-like) +K417N AY.98.1 Delta Usher placements: BA.1(1/1); scorpio lineage B.1.617.2 conflicts with inference lineage BA.1
ERR12411096 99.85% BA.1 Probable Omicron (Unassigned) AY.98.1 Delta Usher placements: BA.1(1/1); scorpio found insufficient support to assign a specific lineage
ERR12411097 99.86% BA.1 Delta (B.1.617.2-like) +K417N AY.98.1 Delta Usher placements: BA.1(1/1); scorpio lineage B.1.617.2 conflicts with inference lineage BA.1
ERR12411095 99.84% BA.1 Delta (B.1.617.2-like) +K417N AY.98.1 Delta Usher placements: BA.1(1/1); scorpio lineage B.1.617.2 conflicts with inference lineage BA.1
ERR12411104 99.89% AY.98.1 Delta (B.1.617.2-like) AY.98.1 Delta Usher placements: AY.98.1(1/1)
ERR12411107 99.84% BA.1 Delta (B.1.617.2-like) +K417N AY.98.1 Delta Usher placements: BA.1(1/1); scorpio lineage B.1.617.2 conflicts with inference lineage BA.1
ERR12411102 99.9% AY.98.1 Delta (B.1.617.2-like) AY.98.1 Delta Usher placements: AY.98.1(1/1)
ERR12411101 99.89% AY.98.1 Delta (B.1.617.2-like) AY.98.1 Delta Usher placements: AY.98.1(1/1)

Freyja

The Freyja plot shows the relative SARS-CoV-2 lineage abundance in each sample. Samples suspect for coinfection will illustrate mixed prevalence of two or more variants. The plots below shows the summarized and specific lineages and their corresponding abundance as detected by Freyja.

VirStrain

Samples were analyzed using the VirStrain tool against a database of representative SARS-CoV-2 sequences. The results are summarized in the table below, where the ‘Most Possible Strain’ represents the lineage with the highest Vscore in the initial iteration. Meanwhile, the ‘Other Possible Strain’ is identified by the highest Vscore in subsequent iterations.

Sample Most Possible Strain Other Possible Strain Valid Map Rate
ERR12411100 AY.98.1_B.1.617.2 AY.43 1/93
ERR12411099 AY.25_B.1.617.2; AY.98.1_B.1.617.2 Omicron 2/93
ERR12411098 AY.25_B.1.617.2; AY.98.1_B.1.617.2 Omicron 2/93
ERR12411107 AY.25_B.1.617.2; AY.98.1_B.1.617.2 Omicron 3/93
ERR12411102 AY.98.1_B.1.617.2 Can not detect other strains. NA
ERR12411101 AY.98.1_B.1.617.2 AY.43 1/93
ERR12411096 AY.25_B.1.617.2; AY.98.1_B.1.617.2 Omicron 3/93
ERR12411097 AY.25_B.1.617.2; AY.98.1_B.1.617.2 Omicron 3/93
ERR12411104 AY.25_B.1.617.2; AY.98.1_B.1.617.2 AY.43 1/93
ERR12411106 AY.25_B.1.617.2 Omicron 6/93
ERR12411105 AY.25_B.1.617.2 Omicron 6/93
ERR12411095 AY.25_B.1.617.2; AY.98.1_B.1.617.2 Omicron 3/93

Nucleotide mixture per position

The figure below shows the bammix plot for nucleotide mixtures of the sample/s with potential SARS-CoV-2 variants coinfection. Multiple sites containing heterogenous bases crossing the set threshold (default >20% minor alelle) mixture will be apparent.

Alternative allele fraction

For each lineage-defining mutations

The alternative allele fraction (AAF) determines the number of reads supporting each variant detected in the sample/s. The AAF per mutation of sample/s flagged for SARS-CoV-2 coinfection are shown in the figure.

For each amplicon

The AAF for each amplicon is plotted by getting the average allele fraction for each lineage within the range of that amplicon.

Amplicon sorting

Sample Coverage Pangolin Scorpio Nextclade WHO clade Note
ERR12411105_lineage_A 99.97% AY.98.1 NA AY.98.1 Delta Usher placements: AY.98.1(1/1)
ERR12411105_lineage_B 99.98% B.1.1.529 Probable Omicron (Unassigned) B.1.1.529 Omicron Usher placements: B.1.1.529(1/1); scorpio found insufficient support to assign a specific lineage
ERR12411097_lineage_A 99.98% AY.98.1 NA AY.98.1 Delta Usher placements: AY.98.1(1/1)
ERR12411097_lineage_B 99.98% AY.98 NA B.1.617.2 Delta Usher placements: AY.98(1/1)
ERR12411099_lineage_A 99.98% AY.98.1 NA AY.98.1 Delta Usher placements: AY.98.1(1/1)
ERR12411099_lineage_B 99.99% AY.98 NA B.1.617.2 Delta Usher placements: AY.98(1/1)
ERR12411100_lineage_A 99.97% AY.98.1 Delta (B.1.617.2-like) AY.98.1 Delta Usher placements: AY.98.1(1/1)
ERR12411100_lineage_B 100.0% B.1 NA B.1 NA Usher placements: B.1(1/1)
ERR12411096_lineage_A 99.96% AY.98.1 NA AY.98.1 Delta Usher placements: AY.98.1(1/1)
ERR12411096_lineage_B 99.99% B.1 NA B.1.617 NA Usher placements: B.1(1/1)
ERR12411104_lineage_A 99.98% AY.98.1 Delta (B.1.617.2-like) AY.98.1 Delta Usher placements: AY.98.1(1/1)
ERR12411104_lineage_B 100.0% B.1 NA B.1 NA Usher placements: B.1(3/3)
ERR12411101_lineage_A 99.97% AY.98.1 Delta (B.1.617.2-like) AY.98.1 Delta Usher placements: AY.98.1(1/1)
ERR12411101_lineage_B 99.98% AY.98 Delta (B.1.617.2-like) B.1.617.2 Delta Usher placements: AY.98(1/1)
ERR12411095_lineage_A 99.98% AY.98.1 NA AY.98.1 Delta Usher placements: AY.98.1(1/1)
ERR12411095_lineage_B 99.99% AY.98 NA B.1.617.2 Delta Usher placements: AY.98(1/1)
ERR12411098_lineage_A 99.98% AY.98.1 NA AY.98.1 Delta Usher placements: AY.98.1(1/1)
ERR12411098_lineage_B 99.99% AY.98 NA B.1.617.2 Delta Usher placements: AY.98(1/1)
ERR12411106_lineage_A 99.97% AY.98.1 NA AY.98.1 Delta Usher placements: AY.98.1(1/1)
ERR12411106_lineage_B 99.98% B.1.1.529 Probable Omicron (Unassigned) B.1.1.529 Omicron Usher placements: B.1.1.529(1/1); scorpio found insufficient support to assign a specific lineage
ERR12411107_lineage_A 99.98% AY.98.1 NA AY.98.1 Delta Usher placements: AY.98.1(1/1)
ERR12411107_lineage_B 99.97% B.1.1.529 Probable Omicron (Unassigned) B.1 NA Usher placements: B.1.1.529(2/2); scorpio found insufficient support to assign a specific lineage

References

The tools used in this pipeline are as follows: